The "pre-submission consultation" and "submission of documents" only supports a single iteration, i.e. the application is considered closed after submission is made (Status: Submitted) or if a response from agency is issued (status: Response Issued). A new application has to be made if you wish to follow up on the agencies' issued response.
The intent of these 2 applications is to facilitate queries and the supplementing of documents to agencies and are not to be tapped on as secondary means for additional iterations. Formal response to address non-compliances in an ongoing submission should be made through a reply to Written Direction.